Rapid Biophysical Characterization and NMR Spectroscopy Structural Analysis of Small Proteins from Bacteria and Archaea

Proteins encoded by small open reading frames (sORFs) have a widespread occurrence in diverse microorganisms and can be of high functional importance. However, due to annotation biases and their technically challenging direct detection, these small proteins have been overlooked for a long time and were only recently rediscovered. The currently rapidly growing number of such proteins requires efficient methods to investigate their structure–function relationship. Herein, a method is presented for fast determination of the conformational properties of small proteins. Their small size makes them perfectly amenable for solution-state NMR spectroscopy. NMR spectroscopy can provide detailed information about their conformational states (folded, partially folded, and unstructured). In the context of the priority program on small proteins funded by the German research foundation (SPP2002), 27 small proteins from 9 different bacterial and archaeal organisms have been investigated. It is found that most of these small proteins are unstructured or partially folded. Bioinformatics tools predict that some of these unstructured proteins can potentially fold upon complex formation. A protocol for fast NMR spectroscopy structure elucidation is described for the small proteins that adopt a persistently folded structure by implementation of new NMR technologies, including automated resonance assignment and nonuniform sampling in combination with targeted acquisition.     

Bimodal Detection of Proteins by 129Xe NMR and Fluorescence Spectroscopy

A full understanding of biological phenomena involves sensitive and noninvasive detection. Herein, we report the optimization of a probe for intracellular proteins that combines the advantages of fluorescence and hyperpolarized ¹²⁹Xe NMR spectroscopy detection. The fluorescence detection part is composed of six residues containing a tetracysteine tag (−CCXXCC−) genetically incorporated into the protein of interest and of a small organic molecule, CrAsH. CrAsH becomes fluorescent if it binds to the tetracysteine tag. The part of the biosensor that enables detection by means of ¹²⁹Xe NMR spectroscopy, which is linked to the CrAsH moiety by a spacer, is based on a cryptophane core that is fully suited to reversibly host xenon. Three different peptides, containing the tetracysteine tag and four organic biosensors of different stereochemistry, are benchmarked to propose the best couple that is fully suited for the in vitro detection of proteins.     

Diffusion Profiling of Therapeutic Proteins by Using Solution NMR Spectroscopy

Characterizing changes to structure and behavior is an important aspect of therapeutic protein development. NMR spectroscopy is well suited to study interactions and higher-order structure that could impact biological function and safety. We used NMR diffusion methods to describe the overall behavior of proteins in solution by defining a “diffusion profile” that captures the complexities in diffusion behavior. Diffusion profiles offer a simple means to interpret protein solution behavior as a distribution of sizes and association states. As a characterization method, diffusion profiling is well suited to complement and augment traditional biophysical and NMR methods to probe the solution behavior of therapeutic proteins.     

Artificially Linked Ubiquitin Dimers Characterised Structurally and Dynamically by NMR Spectroscopy

As one of the most prevalent post-translational modifications in eukaryotic cells, ubiquitylation plays vital roles in many cellular processes, such as protein degradation, DNA metabolism, and cell differentiation. Substrate proteins can be tagged by distinct types of polymeric ubiquitin (Ub) chains, which determine the eventual fate of the modified protein. A facile, click chemistry based approach for the efficient generation of linkage-defined Ub chains, including Ub dimers, was recently established. Within these chains, individual Ub moieties are connected through a triazole linkage, rather than the natural isopeptide bond. Herein, it is reported that the conformation of an artificially K48-linked Ub dimer resembles that of the natively linked dimer, with respect to structural and dynamic characteristics, as demonstrated by means of high-resolution NMR spectroscopy. Thus, it is proposed that artificially linked Ub dimers, as generated by this approach, represent potent tools for studying the inherently different properties and functions of distinct Ub chains.     

Substrate Binding Drives Active‐Site Closing of Human Blood Group B Galactosyltransferase as Revealed by Hot‐Spot Labeling and NMR Spectroscopy Experiments

Crystallography has shown that human blood group A (GTA) and B (GTB) glycosyltransferases undergo transitions between “open”, “semiclosed”, and “closed” conformations upon substrate binding. However, the timescales of the corresponding conformational reorientations are unknown. Crystal structures show that the Trp and Met residues are located at “conformational hot spots” of the enzymes. Therefore, we utilized ¹⁵N side‐chain labeling of Trp residues and ¹³C‐methyl labeling of Met residues to study substrate‐induced conformational transitions of GTB. Chemical‐shift perturbations (CSPs) of Met and Trp residues in direct contact with substrate ligands reflect binding kinetics, whereas the CSPs of Met and Trp residues at remote sites reflect conformational changes of the enzyme upon substrate binding. Acceptor binding is fast on the chemical‐shift timescale with rather small CSPs in the range of less than approximately 20 Hz. Donor binding matches the intermediate exchange regime to yield an estimate for exchange rate constants of approximately 200–300 Hz. Donor or acceptor binding to GTB saturated with acceptor or donor substrate, respectively, is slow (<10 Hz), as are coupled protein motions, reflecting mutual allosteric control of donor and acceptor binding. Remote CSPs suggest that substrate binding drives the enzyme into the closed state required for catalysis. These findings should contribute to better understanding of the mechanism of glycosyl transfer of GTA and GTB.     

HPV16 MuE6/E7嵌合蛋白的原核表达、纯化及其免疫效果

目的表达HPV16型MuE6/E7嵌合蛋白,并检测其免疫原性及抗肿瘤活性。方法将构建的重组MuE6/E7蛋白的表达载体转化大肠杆菌BL21(λDE3)进行诱导表达,表达的包涵体蛋白经分离、纯化、变性及复性后,通过离子交换和分子筛层析进行纯化。纯化蛋白经SDS-PAGE、Western blot、HPLC和质谱分析鉴定,并免疫C57BL/6小鼠,检测其免疫原性和抗肿瘤活性。结果重组MuE6/E7蛋白相对分子质量约为21 000,表达量约为23.06%,表达形式为包涵体,经复性、纯化后,纯度达97.17%。免疫3针后,小鼠可产生高滴度的HPV特异性抗体,并且与注射剂量呈正相关。免疫小鼠能抵抗TC-1肿瘤细胞的攻击,并可延长TC-1致瘤小鼠的存活期。结论已表达并纯化了重组MuE6/E7蛋白,其对TC-1致瘤小鼠具有一定的免疫治疗作用,为进一步研制HPV治疗性疫苗奠定了基础。     

Surface Binding of TOTAPOL Assists Structural Investigations of Amyloid Fibrils by Dynamic Nuclear Polarization NMR Spectroscopy

Dynamic nuclear polarization (DNP) NMR can enhance sensitivity but often comes at the price of a substantial loss of resolution. Two major factors affect spectral quality: low‐temperature heterogeneous line broadening and paramagnetic relaxation enhancement (PRE) effects. Investigations by NMR spectroscopy, isothermal titration calorimetry (ITC), and EPR revealed a new substantial affinity of TOTAPOL to amyloid surfaces, very similar to that shown by the fluorescent dye thioflavin‐T (ThT). As a consequence, DNP spectra with remarkably good resolution and still reasonable enhancement could be obtained at very low TOTAPOL concentrations, typically 400 times lower than commonly employed. These spectra yielded several long‐range constraints that were difficult to obtain without DNP. Our findings open up new strategies for structural studies with DNP NMR spectroscopy on amyloids that can bind the biradical with affinity similar to that shown towards ThT.     

Nucleotide Binding Modes in a Motor Protein Revealed by 31P- and 1H-Detected MAS Solid-State NMR Spectroscopy

Protein–nucleic acid interactions play important roles not only in energy-providing reactions, such as ATP hydrolysis, but also in reading, extending, packaging, or repairing genomes. Although they can often be analyzed in detail with X-ray crystallography, complementary methods are needed to visualize them in complexes, which are not crystalline. Here, we show how solid-state NMR spectroscopy can detect and classify protein–nucleic interactions through site-specific ¹H- and ³¹P-detected spectroscopic methods. The sensitivity of ¹H chemical-shift values on noncovalent interactions involved in these molecular recognition processes is exploited allowing us to probe directly the chemical bonding state, an information, which is not directly accessible from an X-ray structure. We show that these methods can characterize interactions in easy-to-prepare sediments of the 708 kDa dodecameric DnaB helicase in complex with ADP:AlF₄⁻:DNA, and this despite the very challenging size of the complex.     

Structural characterization of FCC feeds from Indian refineries by NMR spectroscopy

Fluid catalytic cracking (FCC) feeds from four Indian refineries are structurally characterized by ¹H, gated-decoupled ¹³C, distortionless enhancement by polarization transfer (DEPT) and 2D ¹H–¹³C HETeronuclear CORrelation (HETCOR) and other 2D nuclear magnetic resonance (NMR) methods. Detailed structural analyses are completely supported by a range of NMR information including chemical shifts of ¹H and ¹³C, CH_n type distributions and ¹H –¹³C connectivities. The average structural parameters like branching sites, average number of branching per molecule, average length of side chains, percentage of saturates, aromatics and naphthenes are obtained from these NMR data. A novel approach based on “multipoint spline base line correction” is employed for estimation of naphthenes and n-paraffins that gives better quantitative estimation than the conventional methods. In this paper, importance is given to the study of those structural parameters that plays a key role in cracking chemistry as well as coke forming tendency of the feedstock. To the best of our knowledge, this is the first attempt to characterize and quantitatively estimate compositions of the high boiling fractions of petroleum feed by NMR methods and especially the complex structure of vacuum gas oil (VGO) fractions used in Indian refineries. The importance of this paper is to help in optimizing the product slate of Indian refineries through proper feedstock blending using few hundreds of million metric tons (MMT) of crude oil consisting of blends of light crudes with different heavy crudes and bottom of the barrel due to escalating cost of crudes.     

Structural Analysis of Hepta-, Nona-, and Undeca-Cyclic Aromatic Hydrocarbons by NMR Spectroscopy

Large condensed polycyclic aromatic hydrocarbons (LCPAHs) generally have distorted structures due to steric repulsion between neighboring hydrogen atoms. The distortion may influence their physicochemical properties such as electric conductivity, photoconductivity, and photochromism. Accordingly we have synthesized LCPAHs and analyzed their structure. In the present study, we synthesized an undecacyclic aromatic compound, dibenzo[a,rst]-dinaphtho[2,1,8-klm:1′,2′-o]pentaphene (DDPP) and determined the structure by use of NMR spectroscopy. To assign the ¹H- and ¹³C-NMR chemical shifts completely, we used the HMQC-TOCSY (Heteronuclear Multiple Quantum Coherence-Total Correlation SpectroscopY) method in which the original proton-carbon correlation is relayed to neighboring protons in the same spin-system. Furthermore, we compared the chemical shifts (δs) of the heptacyclic aromatic hydrocarbon, peropyrene, the nonacyclic, violanthrene B (VEB), and the undecacyclic, DDPP, and investigated correlations between their local structure and δs. For the protons in the bay region, the averaged δs decrease as molecular size increases: 9.23 ppm (hepta-) > 9.07 ppm (nona-) > 8.77 ppm (undeca-). Similar change in the δs is also found for the protons in the cove region: 9.37 ppm (nona-) > 8.81 ppm (undeca-). Thus, it is noted that the averaged δs for the protons in the cove region become downfield than those for the protons in the bay region. The findings are explained in terms of the anisotropic effect of the local magnetic field of benzene rings.     

Cyclotide Structures Revealed by NMR,with a Little Help from X-ray Crystallography

This review highlights the predominant role that NMR has had in determining the structures of cyclotides, a fascinating class of macrocyclic peptides found in plants. Cyclotides contain a cystine knot, a compact structural motif that is constrained by three disulfide bonds and able to resist chemical and biological degradation. Their resistance to proteolytic degradation has made cyclotides appealing as drug leads. Herein, we examine the developments that led to the identification and conclusive determination of the disulfide connectivity of cyclotides and describe in detail the structural features of exemplar cyclotides. We also review the role that X-ray crystallography has played in resolving cyclotide structures and describe how racemic crystallography opened up the possibility of obtaining previously inaccessible X-ray structures of cyclotides.     

mRNA and miRNA Profiles of Exosomes from Cultured Tumor Cells Reveal Biomarkers Specific for HPV16-Positive and HPV16-Negative Head and Neck Cancer

Human papillomavirus (HPV)(+) and HPV(−) head and neck cancer (HNC) cells’ interactions with the host immune system are poorly understood. Recently, we identified molecular and functional differences in exosomes produced by HPV(+) vs. HPV(−) cells, suggesting that genetic cargos of exosomes might identify novel biomarkers in HPV-related HNCs. Exosomes were isolated by size exclusion chromatography from supernatants of three HPV(+) and two HPV(−) HNC cell lines. Paired cell lysates and exosomes were analyzed for messenger RNA (mRNA) by qRT-PCR and microRNA (miR) contents by nanostring analysis. The mRNA profiles of HPV(+) vs. HPV(−) cells were distinct, with EGFR, TP53 and HSPA1A/B overexpressed in HPV(+) cells and IL6, FAS and DPP4 in HPV(−) cells. The mRNA profiles of HPV(+) or HPV(−) exosomes resembled the cargo of their parent cells. miR expression profiles in cell lysates identified 8 miRs expressed in HPV(−) cells vs. 14 miRs in HPV(+) cells. miR-205-5p was exclusively expressed in HPV(+) exosomes, and miR-1972 was only detected in HPV(−) exosomes. We showed that HPV(+) and HPV(−) exosomes recapitulated the mRNA expression profiles of their parent cells. Expression of miRs was dependent on the HPV status, and miR-205-5p in HPV(+) and miR-1972 in HPV(−) exosomes emerge as potential discriminating HPV-associated biomarkers.     

Specific isotope labeling of colicin E1 and B channel domains for membrane topological analysis by oriented solid-state NMR spectroscopy

An approach is presented to selectively label the methionines of the colicin E1 and B channel domains, each about 200 residues in size, and use them for oriented solid-state NMR investigations. By combining site-directed mutagenesis, bacterial overexpression in a methionine auxotroph E. coli strain and biochemical purification, quantitative amounts of the proteins for NMR structural investigations were obtained. The proteins were selectively labeled with (15)N at only one, or at a few, selected sites. Multidimensional heteronuclear correlation high-resolution NMR spectroscopy and mass spectrometry were used to monitor the quality of isotopic labeling. Thereafter the proteins were reconstituted into oriented phospholipid bilayers and investigated by proton-decoupled (15)N solid-state NMR spectroscopy. The colicin E1 thermolytic fragment that carries a single (15)N methionine within its hydrophobic helix 9 region exhibited (15)N resonances that are characteristic of helices that are oriented predominantly parallel to the membrane surface at low temperature, and a variety of alignments and conformations at room temperature. This suggests that the protein can adopt both umbrella and pen-knife conformations.     

The Casein Kinase 2‐Dependent Phosphorylation of NS5A Domain 3 from Hepatitis C Virus Followed by Time‐Resolved NMR Spectroscopy

Hepatitis C virus (HCV) chronically affects millions of individuals worldwide. The HCV nonstructural protein 5A (NS5A) plays a critical role in the viral assembly pathway. Domain 3 (D3) of NS5A is an unstructured polypeptide responsible for the interaction with the core particle assembly structure. Casein kinase 2 (CK2) phosphorylates NS5A‐D3 at multiple sites that have mostly been predicted and only observed indirectly. In order to identify the CK2‐dependent phosphorylation sites, we monitored the reaction between NS5A‐D3 and CK2 in vitro by time‐resolved NMR. We unambiguously identified four serine residues as substrates of CK2. The apparent rate constant for each site was determined from the reaction curves. Ser408 was quickly phosphorylated, whereas the three other serine residues reacted more slowly. These results provide a starting point from which to elucidate the role of phosphorylation in the mechanisms of viral assembly—and in the modulation of the viral activity—at the molecular level.     

Interactions between S100A9 and Alpha-Synuclein: Insight from NMR Spectroscopy

S100A9 is a pro-inflammatory protein that co-aggregates with other proteins in amyloid fibril plaques. S100A9 can influence the aggregation kinetics and amyloid fibril structure of alpha-synuclein (α-syn), which is involved in Parkinson’s disease. Currently, there are limited data regarding their cross-interaction and how it influences the aggregation process. In this work, we analyzed this interaction using solution 19F and 2D ¹⁵N–¹H HSQC NMR spectroscopy and studied the aggregation properties of these two proteins. Here, we show that α-syn interacts with S100A9 at specific regions, which are also essential in the first step of aggregation. We also demonstrate that the 4-fluorophenylalanine label in alpha-synuclein is a sensitive probe to study interaction and aggregation using 19F NMR spectroscopy.